the genereader: a complete ngs system for your lab, live...
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Sample to Insight
The GeneReader:A Complete NGS System for Your Lab, Live in 30 Days
Sylvain Cogne / Massimo Cerfeda
Market Development Manager NGS, EMEA
May 2017
12016 Analyst & Investor Day
Sample to Insight2016 Analyst & Investor Day 2
Customers want meaningful molecular insights
Moving from tools and components to solutions that provide valuable insights
BIOLOGICAL SAMPLE
VALUABLE MOLECULAR
INSIGHTS
Sample Technologies Assay Technologies
Bioinformatics Automation systems
SAMPLE TO INSIGHT SOLUTIONS
Faster Better More efficiently
Situation
Sample to Insight
Sample InsightSampleQC
LibraryQC
VariantConfirmation
The GeneReader NGS Sample to Insight solution
The GeneReader™ NGS System is the first complete Sample to Insight®
NGS solution designed for any lab to deliver actionable insights
Confidential
Sample to InsightConfidential
Workflow overview – Template Sequencing
Sequencing by synthesis technology Automated on GeneReader 1-3 Flowcells in parallel 16 samples per flowcell 16 million reads per flowcell 100-150 bp maximum read length 85% of bases > Q25 Continuous loading mode Generate FASTQ files Auto transfer to QCI-A
SequencingDNAExtraction
TargetEnrichment
ClonalAmplification
LibraryPreparation
Analysis /Interpretation
GR 1.1 specifications
Sample to Insight5
• LIMS connectivity, iPad-based manual
• True ‘actionability’
The GeneReader NGS System is intended for Research Use Only. Not for use in diagnostic procedures
• Robust and consistent performance
• Bioinformatics & Reporting
Sample to Insight
The ultimate objective of NGS in molecular pathology
6GeneReader NGS System PROM-10229-001
A full Sample Report in your hands• Simple • Actionable• Yet comprehensive
Sample to Insight
Not a Sequencer---but a System
GeneReader NGS System PROM-9303-002 7
Nucleic Acid
Extraction
TargetEnrichment
LibraryPreparation
Next-GenerationSequencing
DataAnalysis Interpretation
QIAxcel QIAxcelRGQQC
GeneRead Assistant (iPad and App included)
Support
Data Management
GeneRead Link and LIMS
QIAcube QIAcubeRGQ GeneRead QIAcube
GeneReader QCI-Analyze QCI-Interpret
Automation
Sample to InsightQIAGEN | qiagenbioinformatics.com | [email protected] | qiagen.com | 2016 8
Designed, built and validated in collaboration with clinical labs
Customizable Reporting ability to capture /persist internal annotations,
integration into LIMS and EMR systems
Comprehensive Curation of Clinical Evidence
reported cases, drug labels, professional guidelines
Decision Support Softwareclassify variants, identify treatment options, and
geographical clinical-trial matching
Treatment and Trial Identification based upon levels of evidence, expected drug
response, prognosis and lab defined rules
QCII – Intuitive and transparent variant interpretation
Sample to Insight
The QIAGEN Knowledge Base
Title, Location, Date 9
18+ years experience in content acquisition and ontology
Knowledge BaseFindings
>13,000,000
>30,000 Publications
>340,000 Samples Analyzed
>20,000 Disease Classes
>30 IntegratedDatabases
>200MDs, PhDs
Automated & Manual Curation
Sample to Insight
GeneRead Link
GeneReader NGS System PROM-9303-002 10
Workflow management solution for the GeneReader NGS System
Automated transfer of data from LIMS and of results back to LIMS
Electronic lab notebook for complete traceability
Full sample and workflow tracking
Result and QC score mgmt. with recommendation for actions
Minimal manual interaction for data handling
Sample to Insight
GeneRead Link
GeneReader NGS System PROM-9303-002 11
The entire workflow on one screenIntegratedActionableFlexibleAffordableReliable
ABLHC
Workflow phases overview always visible
Work to doSamples waiting in this phase
Work in ProgressGuided execution for sample batch
Results to Approve Based on execution results and QC
Sample to Insight
QIAact panel portfolio: maximum actionability within 30 days
Title, Location, Date 12
Actionable Insights Tumor Panel
Lung DNA & compr. Fusions Panel
Myeloid Leukemia Panel
BRCA 1/2 Panel
Custom Panel
Based on QIAGEN knowledge base, enabling maximum actionability Verified from sample to insight, enabling any lab to go live within 30 days
IntegratedActionableFlexibleAffordableReliable
ABLHC
Sample to Insight
Every GR assay undergoes rigid sample to insight verification
13
Systematic Sample-to-Insight verification by multiple experiments, Instruments, users and sites and reviewed on Subsystem and undergo System approval, before going to release
Sample to Insight
QIAact BRCA precision study
14
Very good reproducibility between batches, operators and systems
Sample to Insight
Robust data of the workflow (HotSpot Panel)
PROM-10667-001 USCAP March 2017 For Research Use Only; Now available in the US with NEW chemistry 15
Achieved consistently high performance regardless of variables* in:• Sample batch• Operator and experience level• Instrument and site• Plexing (1-10 samples per flow cell)
* 3 batches of Horizon material, 3 sites/instruments, 3 operators
Sample to Insight
Chr Gene VariantExpected Allelic
Frequency(ddPCR Range)*
GeneReader (ActioanableInsights Tumor Panel)
Observed frequency*(Standard Deviation)
Average Coverage
3rd PartyVerification(ddPCR)**
7p12 EGFR L858R 1.00%(0.6-1.4%)
1.29%(0.29%) 6,195 0.98
7p12 EGFR ΔE746 - A750 1.00%(0.6-1.4%)
1.28%(0.12%) 10,340 1.09
7p12 EGFR T790M 1.00%(0.6-1.4%)
0.97%(0.04%) 1,226 1.00
7p12 EGFR V769 -D770insASV
1.00%(0.6-1.4%)
0.86%(0.01%) 4,351 0.89
12p12.1 KRAS G12D 1.30%(0.78-1.82%)
1.32%(0.39%) 10,527 1.22
1p13.2 NRAS Q61K 1.30%(0.78-1.82%)
1.64%(0.12%) 11,757 1,25
1p13.2 NRAS A59T 1.30%(0.78-1.82%)
1.34%(0.08%) 10,552 1.20
3q26.3 PIK3CA E545K 1.30%(0.78-1.82%)
1.58%(0.05%) 36,384 1.41
Liquid Biopsy Data with Equally Rigorous Testing
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cfDNA samples at ~1%
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*: 6-plex
Accurately, consistently and robustly detecting cfDNA at 1% sensitivity per design specification
PROM-10622-001 Precision Medicine Webinar For Research Use Only; Now available in the US with NEW chemistry
Sample to Insight
Our data quality exceeds latest Palmetto standards
PROM-10622-001 Precision Medicine Webinar For Research Use Only; Now available in the US with NEW 17
Sample to Insight
QIAact panel portfolio: maximum actionability within 30 days
Title, Location, Date 18
Actionable Insights Tumor Panel
Lung DNA & compr. Fusions Panel
Myeloid Leukemia Panel
BRCA 1/2 Panel
Custom Panel
Based on QIAGEN knowledge base, enabling maximum actionability Verified from sample to insight, enabling any lab to go live within 30 days
IntegratedActionableFlexibleAffordableReliable
ABLHC
Sample to Insight
Most actionable panel for first-line testing
GeneReader NGS System PROM-9303-002 19
• KRAS
• NRAS
• KIT
• BRAF
• PDGFRA
• ALK
• EGFR
• ERBB2
• PIK3CA
• ERBB3
• ESR1
• RAF1
Targeting solid tumors with:• Highest prevalence
• Greatest need for testing
• Variants associated with actionable insights
12 genes
QIAGENKnowledge Base
Lung
Breast
Ovarian Colorectal
Melanoma
Sample to Insight
QIAact Lung Panel on GeneReader NGS System
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Number of VariantsGenes QIAact Lung DNA Panel VOIs QIAact AIT V2 VOIsNRAS 20 41NTRK1 3 0DDR2 2 0ALK 30 39RAF1 0 2PIK3CA 14 167PDGFRA 1 47KIT 17 257RICTOR (CNV) 0ROS1 3 0ESR1 6 11EGFR 325 (+CNV) 466MET 20 (+CNV) 0BRAF 22 157FGFR1 (CNV) 0PTEN 1 0KRAS 66 152ERBB3 0 10AKT1 1 0MAP2K1 14 0ERBB2 4 (+CNV) 62Total Variants 549 1411
QIAact Lung panel covers more Lung relevant variants
Sample to Insight21
Thank you
Questions?
GeneReader NGS System PROM-9303-002
Sample to Insight22
Additionals
GeneReader NGS System PROM-9303-002
Sample to Insight
DNAExtraction
Confidential
23
Workflow overview – target enrichment
Gene Panels – focus on the genomic region of interest
TargetEnrichment
ClonalAmplification SequencingLibrary
PreparationAnalysis /
Interpretation
GR 1.0 specifications as shared in May 2016
QIAact V2.0 Assay technology
Sample to Insight
Actionable Insights Tumor Panel RAS sample study
GeneReader NGS System PROM-9303-002 24
Outstanding coverage achieved even with challenging FFPE samples
Parameter Detail
Instrument 3 GeneReader NGS Systems
Reagents GeneReader Reagents
Bioinformatics solution QCI-Analyze, QCI-Interpret
Sample number and type 43 FFPE Colorectal Cancer (CRC) samples
Sample age 3 to 20 years
Sample quality Highly fragmented DNA
Variant insight coverage 98.6% of bases covered at >500x99.8% of bases covered at >200x
IntegratedActionableFlexibleAffordableReliable
ABLHC
Sample to Insight
Parameter Detail
Instrument 5 GeneReader NGS Systems
Reagents GeneReader Reagents
Bioinformatics solution QCI-Analyze, QCI-Interpret
Sample number and type 39 FFPE Colorectal Cancer (CRC) samples
Sample age 3 to 20 years
Sample quality Highly fragmented DNA
Amplicon coverage 94.45% of bases covered at >500x97.27% of bases covered at >200x
Variant insight coverage 99.36% of bases covered at >500x99.89% of bases covered at >200x
QIAact V2.0 - RAS Sample Study
Note: Positive samples included into the study have all been confirmed with Sanger sequencing and passed Quantimize <0.04. ) For the repeat study performed with updated sequencing chemistry, four wildtype samples were not available anymore reducing the sample number to 39 compared to results shown earlier.
Outstanding coverage achieved even with challenging FFPE samples
Sample to Insight
QIAact V2.0 - RAS concordance study with therascreen
Confidential
RAS agreement study
>5% Ras variant Allele Frequency Cutoff
therascreen PCR and Pyro Assays (1)
+ (MT) –(WT) Total
GeneReader NGS System (2)
+ (MT) 14 0 14
– (WT) 0 25 25
Total 14 25 39
Note: (1) If KRAS status regarded as mutant (MT) as identified by either therascreen KRAS PCR Assay or by therascreen RAS Extension Pyro Assay. (2) Variants from codons 12, 13, 59, 61, 117, 146 contained in established QIAGEN therascreen assays are called.
100 % Agreement between GeneReader NGS System and QIAGEN therascreen PCR & Pyro Assays
Sample to Insight
QIAact BRCA 1/2 Panel: not just for Inherited Breast Cancer
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Cancer Types Mutation TypesNCCN/SGO Guidelines on Testing
Clinical Actionability
• Breast• Ovarian
• Germline• Somatic
• All patients with Ovarian
• Patients with high-risk Breast Cancer
• PARP inhibitor
• Active trials for somatic mutations
Need to detect mutations in blood & FFPE and in multiple cancer types
Sample to Insight
QIAact BRCA Performance on GeneReader NGS System
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QIAact BRCA 1/2On GeneReader NGS System
VAF cut off >=5% (in FFPE)
ROI full exons + 20bp flanking
True Positives 274
False Positives 0
False Negatives 0
PPV 100 %
Sensitivity 100 %
Accuracy 100%
Coverage of ROI 98.84% @ 5% LAF99.84% @ 10% LAF
showing 100% PPV and PPA @ VAF of 5%
Sample to Insight
QCI Provides Clear Insights Into Variant Pathogenicity
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Variant list screen shows overview of validated variants Colour coded classification of variants Complete transparency of classification evidence Actionable variants highlighted
QIAGEN-AZ confidential
Sample to Insight
QCI Provides Clear Insights Into Variant Pathogenicity
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See approved drugs from EMA, FDA, ESMO, ASCO and NCCN (configurable) See clinical trials specific to geographical location
QIAGEN-AZ confidential
Sample to Insight
QIAact Lung All-in-One Assay – need for test consolidation
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Complex genetic changes. Examples:Point mutation: EGFR T790M
Large deletion: MET: exon 14
CNV: ALK
Fusion: RET, ROS1
Tests typically deployed:• PCR• IHC• FISH• Array
Need for one single assay that includes all the results
Sample to Insight
QIAact Lung DNA Panel Specifications
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KPI Specification
Actionable mutations 100% (~ 550)
SNV Detection Yes
Small Indel Detection (<6 bp) Yes
Large Indel Detection (<18 bp) Yes
CNV Yes
VAF Threshold 5% (FFPE), <1% (LB)
Specificity >90%
Variant Coverage >1000x 99%; >100x 99% UMIs
Fusion Yes (via RNA Seq)
Sample to Insight
QIAact Lung RNA Panel for the GeneReader NGS System
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Fusions of InterestsQIAact Lung RNA Panel
Total number of genes 72
Total number of 5‘ partners 60
Total number of 3‘ partners 14
Total number of fusions 77
Frequency cut off 20% tumor cells in wild type background
QIAact Lung DNA Panel + QIAact Lung RNA Panel = QIAact Lung All-in-One Assay